Naruto the Third Prototype
by Animewar
Summary: What happens when Naruto strikes up a deal with the Kyuubi and gains a new strand of the Blacklight virus. Rated M for violence and some gore
1. Chapter 1

Prologue

It's been eight years sense the Kyuubi attack and as usual the festival was being held to honor the Fourth Hokage who killed the mighty beast. At this festival there are many stands for food games and the, such and all but a few people where their. The men and women of the civilian council decided to have a meeting to day on something important, important enough have the entire Shinobi council and the Third Hokage present.

Hiruzen Sarutobi was _NOT_ in a good mood. For starters he never liked sitting in on the debates of the civilian council as they have nothing to do the, activates of the Shinobi community. Secondly they called this meeting almost an hour ago and have yet to explain why they needed the Shinobi council to sit in. suddenly the doors open as a man comes rushing inside the council room. At the sight of this the civilian council starts to become worried, while the Hokage and the Shinobi council is confused

"Hokage-sama, Hokage-sama, please hurry theirs a mob outside and they are trying to kill Naruto," said the man the Hokages eyes go wide.

"I want none of you to leave this room until I say other wise" yelled the Hokage before rushing out of the room.

* One and a half hours ago *

A young boy no older than eight was walking the empty streets of Konoha. This boy was Naruto Uzumaki the Kyuubi Jinchuuriki, but even he doesn't know that. Instead he questions why the villagers hate him, as he has done nothing wrong. He constantly be thrown out of stores just for entering, he would be called things like 'Demon', 'Monster', or 'That thing'. Even the orphanage had kicked him out about two years ago where he wondered the streets for weeks scavenging for food, or finding a nice box to sleep in. After about five minutes of walking Naruto returns to his apartment that the Third had given him. The apartment room had noting special in it just a bed with a single pillow and a light blanket, a small kitchen with a fridge, with next to nothing inside but a carton of expired milk, and an egg or two. Naruto lays down on his bed know what today was and what was to come.

Today was Naruto's birthday a day, and every year the villagers give him the same 'present' a beating by a mob. So laying on his bed Naruto starts to sing to him self with a day voice.

"Happy birthday to me . . . Happy birthday to me . . . Happy birthday dear Naruto . . . Happy birthday to me." As he end a single silent tears forms and falls down his cheek. He then falls asleep hungry like most nights. About an hour later there was yelling outside his apartment, as the mob appeared pounding on the door waking Naruto up. Before long the door was broken down and he was dragged outside by his shirt, he never even attempted to leave or struggle. He was then cut stabbed beaten with many different objects and even had more than one empty bottle of sake thrown at him. All the while Naruto never uttered a sound, no yelling, no cries of pain, nothing. Before long after they got tired of that the had two of the adults hold his arms keeping him on his knees, then one of the men took out a pocketknife and cut out his right eye. At this Naruto was let go and was rolling on the ground in pain holding where the eye used to be. And before he knew it his instincts kicked in and he started to run. The mob saw this and ran after him before catching up to him in front of the raman stand. The owner when he started to hear some noise coming from out side saw the mob and decided to go straight to the Hokage. Soon after he left though one of them had gotten a hold of a sword. He had hi held up again and swung down cutting cleanly through his left arm deciding their work was done they all went home back to their families, leaving Naruto bleeding to death. That was the scene the Third saw when him and two AMBU found him before rushing him the hospital.

* Naruto's Mindscape *

Naruto wakes up in what looks to be a swear, with the floor covered in water. Deciding to look around he comes across a gigantic cage of sorts and over where the two half's of the door meet is a piece a paper with the word 'seal' written on it. Naruto is intrigued by this wondering what could behind the bars. When he got close enough to touch it he a deafening roar was heard from behind. Naruto stumble back a bit holding his ears in pain, when it stopped all he heard was laughter in a very deep voice.

"**So child you have come**"

"W-who a-a-are you?" Naruto asked weakly

"**Bow you insolent human before the might to the Kyuubi no Kitsune!**" Yelled the Kyuubi arrogantly

"W-why are you h-here" said Naruto starting to gain some strength in is voice "and w-where is this place"

"**This is your own mind you damn fool!**" Kyuubi yelled

"Weren't you taught about using your inside voice?" asked Naruto sarcastically. The Kyuubi just stares at him before laughing.

"**I'm starting to like you Kit.**" He said after calming down a bit

"So why am I here?" Naruto Asked

"**Well I would guess you're here because of the trauma you just had the misfortune to go through.**" Said the Kyuubi but Naruto just stared at him with a blank expression on his face wondering what he was talking about. "**You have know idea what I'm talking about do you?**" he asked

"Nope" said Naruto bluntly "not a clue"

"**Not that surprising given how tragic your wounds are.**" Said Kyuubi "**Well it's about time you woke up."** Kyuubi finished then everything goes black. A short time later he slowly starts to open his eyes.

* Day after the Hokage found Naruto *

The Third Hokage was in the hospital sitting next to Naruto Uzumaki. And the only emotions that he was showing were that of sorrow and a furious passion to kill every member of the Civilian Council. So in a nutshell the Hokage was _pissed_. Because not one hour ago he held another council meeting to know what happened to the blonde.

After much debating they found out that most of the Civilian Council, paid those who had done so much damage to he boy, the other knew about but didn't care. During the whole meeting the Hokage wanted to have to the Shinobi Council kill the Civilian Council just out of principle.

Now though he just wanted Naruto to pull through when suddenly Naruto body starts to move.

"W-what ha-happened last n-night?" Naruto asked weakly to no one as he started to stand up

"Naruto your awake." Stated Sarutobi "I'm sorry to have to tell you this but I'm afraid your going to have to quit your education to be a Shinobi." He said with much sadness in his voice

"W-what do you mean Jiji-san?" Naruto asked

"I'm sorry but I'm afraid the mob who attacked you last night severed your left arm after they took out your right eye." Said the Third looking at the floor in shame. Naruto not believing this reached for his left arm but found only a stump remaining, then went for his eye to find not resistance of any kind as he pushed the bandages in. the Hokage stood up and told Naruto "I wish that I could stay longer but I still have my duty to perform as Hokage." he then goes for the door and opens it saying one last thing before leaving

"I'm sorry."

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hey please remember to review I like to know what people think of the story so far.


	2. Chapter 2

Hello here's another one for you

Disclaimer: I do not own Naruto or prototype but I wish I did

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Chapter 1

Two months have passed sense the 'incident'. In the first week that Naruto stayed in the hospital the Hokage visited him about five of those days. In those days he tried to get Naruto to talk again, but was unsuccessful. Naruto was all but mute at this point. But one thing that the Hokage didn't know until about a month later is that Naruto had tried to commit suicide almost ten times total. This caused the Hokage feel even worse about what happened. The Hokage after the month was in the hospital decided to replace most of the civilian council sense it was their plan to have Naruto die the day that he was attacked.

The attack even went so far as to effect the academy. After the first week the class was wondering what happened to Naruto, but all Iruka told them was that he was in the hospital for some injury he received. The class never asked or was worried about what could have caused him to be in the hospital. Well all but Hinata Hyuga who was worried sick about her crush, but was too shy to say anything about the issue so eventually it was just never spoken about in class.

Now after all the attempts at suicide the hospital moved him into a special room where the wall were padded and the only thing in the room was a bed on the floor with a single pillow and no blanket. The reason this room has no blanket was be cause the room had a special seal on the ceilings to keep the room at a constant temperature. Every so often a nurse would check up on him but all they would see him do is sit on the floor and stare the ceiling with a blank expression.

* Hospital *

The Hokage was making another trip to see Naruto as he was walking down the halls to room he could hear whispers from two of the nurses.

"Hey what's the Hokage doing here?" one said to the another nurse

"Your new here aren't you?" the other nurse asked. Her friend only nodded. "Well he's been visiting _him_ almost everyday for almost a hour." That all the Hokage heard before and head splitting scream. The Sarutobi went wide-eyed recognizing that as Naruto's voice before he took of running. When he got to the room he could see three nurses holing him down while another attempted to give him a sedative.

* Five minutes earlier in Naruto's room *

Naruto was laying down on the bed asleep before being pulled into his mindscape. He arrived he was right in front of the Kyuubi's cage the difference between when he was their the first time was that, the room was darker, their was more water on the ground when he walked up to the cage all he could see was the Kyuubi's glowing eyes.

"**What do you think you've been doing?**" said the Kyuubi in such a manner of that of a parent

"What are you talking about?" Asked Naruto slightly confused

"**I'm talking about you trying to kill yourself you brat!**" He yelled

"Why do you even care you big fur ball." Retorted Naruto

"**YOU INSOLENT WHELP HOW DARE YOU SPEAK TO ME THE GREAT KYUUBI NO KITSUNE LIKE THAT!**" Yelled the Kyuubi loud enough to move some of the water. "**Kit I only care because if you die I die.**" Said the Kyuubi after calming down.

"But I have reason no to live, the only thing I could look forward to in life was becoming a Shinobi." Said Naruto in a monotone voice

"**Then how about I give you a second chance.**" Kyuubi said

"What are you talking about?" Naruto asked

"**Well you see many thousands of years ago after the time of the Sage of Six Paths, I found myself in another more advanced world their I saw two individuals able to transform their bodies battling on the top of building taller than any in this miserable village.**" "**After the winner was decided and he left I went to the battle ground.**" "**When I touched the blood it seemed to be almost alive and latch onto me.**" "**It seemed to want to transform me in a way but because it seems to only work on living creature, I am not living just a mass of Chakra in the form of a fox.**" "**So it's been trying to kill me off for years, but is unable to.**" Finished the Kyuubi

"So how does that help me?" Asked Naruto wondering if there was a point in the Kyuubi's story

"**I'm saying that I could give you the virus in doing so you could have unimaginable power, and an even greater ability to heal even from such injures such as the ones you have now.**" Said the Kyuubi

"Why would you want to give me power?" Asked Naruto skeptical

"**I'll be honest with you, I don't like you in any sense of the word, but I also don't want to has a week vessel.**" said the Kyuubi "**So will you accept the virus and become strong or will you continue to be weak?**"

"I choose," started Naruto "the virus"

"**Good, good**" said the Kyuubi and on his command the virus takes hold of Naruto and that's when the pain starts, so much that it forces Naruto back into the real world. When his eyes open he continues his screaming from in the mindscape. Almost immediately four nurses come running inside with some sedatives. Right after the needle was put into his skin Sarutobi came barging into the room. Unfortunately the sedative does not work and the nurses back off as Naruto rolls onto the floor. After about a minute of screaming Naruto finally stops, and is asleep.

The nurses then strap Naruto to a few machines to monitor him. The entire rest of the day the Hokage was sitting by Naruto's side hoping for him to get better.

* Naruto's mindscape *

Naruto goes back to the Kyuubi cage. "Hey did it work?' he asked

"Yes it did now there are a few things I need to explain first . . ." said the Kyuubi he then talks to Naruto about what Naruto can do now from running at high speeds with out chakra, even running up buildings, to his only real 'power' called Consuming. When it was all over and done with Naruto thanked the Kyuubi and proceeded to go back to he real world to sleep.

* The next morning *

Naruto wakes up to find him strapped to different machines the biggest one is the one to monitor his heart rate. When he looks around his room he sees Sarutobi asleep in a chair next to his bed.

When Sarutobi woke you he saw that Naruto was sitting up looking at the wall parallel to him. "How do you feel?" he asked

"Well enough," said Naruto "But you must be wondering what caused me to scream like that." He continued

"Do you know what happened?" the Hokage started to say "the doctors can't find anything wrong you."

"Well you see Hokage-jiji I made a deal with the Kyuubi." Said Naruto Sarutobi went wide-eyed not knowing that Naruto knew. "He gave me a new ability not ever seen in this realm." "But this ability I now have has a power that can fix both my arm and my eye." The Hokages eyes went wide a saucers hearing this news think that is too true to be real. "Unfortunately I need to something called 'Consuming' where I take another Bio Mass and turn it into my own." Naruto finished

"What do you mean Bio Mass?" Asked the Hokage

"Bio Mass basically means the DNA of any living creature or human." Said Naruto "Unfortunately a side effect of consuming a human is you gain all their memories though you only see one or two of them their still their." Said Naruto "Now the only way to fix me in this state would be to consume a living being."

"I'm sorry Naruto but you can't eat another Human that is called cannibalism and is punishable by death."

"Consuming and eating are not the same thing Hokage-jiji, eating is ingesting through the mouth, but consuming is you more like absorbing the person, though your body."

"I'm sorry Naruto but it's not something I can believe," replied the Hokage

"If you let me I can show you," started Naruto "You can just use a prisoner or a man who needs to be interrogated." Said Naruto. The Hokage considers this but tells Naruto to wait till tomorrow for his answer. The Hokage then strolls down to the T&I department (Torture and Interrogation).

Ibiki was having a decent day going though some of his daily scheduled interrogations unfortunately his next one has been tricky to work with, as he's not been saying anything of importance. He's walking down the hallway to drop off a form to request a Yamanaka to get the info. That's when he noticed the Hokage a rare sight to see in the department.

"Hello Hokage-sama, what might I help you with?" Asked Ibiki

"Yes I heard that you've been having trouble getting information, which is rare indeed." Said the Hokage

"Ah yes that would be the spy we caught about four months ago." Said Ibiki "It looks like theirs a lock on his mind or something, I'm headed over to the desk right now o request a Yamanaka to come in." Ibiki finished

"Actually I wish you'd put that off I may have found something better than a Yamanaka for getting into someone's memory." Said the Hokage "And with your permission I will being him in tomorrow."

"Well if he's as good as you say he is I'll give him a chance," said Ibiki "when should I expect him here?" he then asked

"Tomorrow at around noon, is when I will be bring him here and make sure it's a room with a one way window." Said the Hokage "I'm wondering myself on how he's going to get the information."

"Well sir if that's all I'll take my leave." Said Ibiki walking away. The Hokage then went to his office to get the paper work ready to release Naruto from the hospital.

* The next morning, in Konoha's Hospital *

Naruto woke up early which surprised him at first. He then went to doing what he normally does and stares around room doing things like counting the dots on the ceiling. About half an hour into it a knocking comes at the door. It then opens to show The Third walking in with a wheelchair and stopping in front of the bed.

"Come on Naruto you are being released and will be taken to the T&I department to see if your consume ability is real." He said, Naruto nodded before the Hokage picked him up and placed him the chair. They proceeded to get out of the hospital and into the streets. Due to the time know one was out for any type of activities yet. It's about a good forty-five minutes later before they reached the department their they saw Ibiki already their waiting for them.

"This is him?" asked Ibiki in disbelieve that some one as crippled and young as this boy can do what only a very experienced Yamanaka can do.

"Trust me I believe he can do it." Said they Hokage Ibiki just shrugged as they went to the man's holding cell. The Shinobi in the cell looked up when the he heard the cell doors open and close again when he did he Naruto standing over him with Ibiki and the Hokage behind him the nin starts to laugh at this.

"So you really think a kid is going to interrogate me, that's rich." He said struggling to say each word though his laughter.

"No I wont be interrogating you, I'm going to do worse" said Naruto as a smile came across his face "_Uirusu: Shouhi_ (_Virus: Consume_)" as he said those word black and red tendril came out of him what seemed to eat the man leaving only a spot of blood on the floor after the consuming process was complete Naruto held his head inn pain as he received a memory from the man.

* Flashback starts *

"_How may I serve you my lord?" said the Shinobi to a man whose face was covered in shadows the man laughed before saying_

"_You are to infiltrate the Konoha and make contact with one of my spies their, the Shinobi teacher, their you ask about his mission to get the Sacred Scroll of Sealing." the man said in a voice that con only be described as slimy an just wrong._

* Flashback ends *

When Naruto comes to more black and red tendrils appear from his stump and from his eye-socket they then from the missing eye and arm making it look like the damage never happened "Finally Their back" said Naruto looking at his new left hand while this was happening Ibiki was staring at him wide-eyed along with Sarutobi. After getting over the shock of what just happened Ibiki asks Naruto

"Did you get any information out of that?"

"Yes actually I learned that he was meeting with a spy within the village to ask about his mission to gain the Sacred Scroll of Sealing." Said Naruto "I also know that the person he was meeting with was a teacher here in the Ninja Academy, and with your permission I would like to continue my time in the Academy while looking for the infiltrator."

"I could understand returning to the Academy but to look for the infiltrator?" asked the Hokage

"Yes I believe that the infiltrator has a locked mind similar or more advanced than the one I just consumed, and if the teacher are anything like I remember about them then I know that they would want to use me to get the scroll before killing me and taking the scroll."

"Yes I think that may work out but I want you to come to me with any suspicious about any of the teachers." Said Sarutobi

"Yes Hokage-sama" said Naruto bowing "Now if you don't mind I have a class I need to get to."

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Please review I do like to know peoples opinions on some things, that are for contructive critisisms.

And the whole Virus: consume thing I put in thier was because I thought something like that would fit wel in Naruto as they sually say attack names befor ethey uses them.


	3. Chapter 3

thank you Ultimate-Zelda-fan, firelordeg, InsanexAngel, Wolfone10, windfox90. for your reviews, and sorry to the ones i missed for the last chapter. Also for thos who are wondering thier will most likly be no pairings in this, if I do make one with Naruto it will be NaruXHina

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Chapter 2

The Next four years in the Ninja Academy went by fast, the day Naruto returned he interrupted the class in the middle of a lecture and calmly walked over and sat in the empty seat. Naturally Iruka was wide-eyed as was the rest of the class, although Hinata looked relived. So after taking the graduation test twice and failing them both Naruto was able to see which teachers were suspicious, in the end he decided it was either Misuki, or Iruka who could not be trusted, although Naruto was more sure of it being Misuki, as he tries to fail him, while Iruka actually tries to help him. Now Naruto has over time gotten more and more elaborate in his pranks, as his last was painting the Hokage mountainside, now once again Naruto is inside the testing room for the graduation exam as he already took the written portion of the exam. "You know the drill Naruto," said Iruka behind the desk, "You must make at least two _Bushins_ (_Clones_) to pass" so Naruto starts to close his eyes ad starts concentrating his chakra and cries out the jutsu's name.

"_Bushin no Jutsu!_" He opens his eyes and look to his left to see one clone that was very pale in color and looked almost dead Iruka then gets a tick mark on his forehead before yelling

"You fail!"

"Ah can't you cut him a break this time Iruka" came the calm voice of Misuki as Naruto showed fake hope in his eyes

"No Misuki I can't the other students were each able to make at least two or three clone." "Granted Naruto did make a clone, he was only able t make one and it's poor at best, I simply can not allow Naruto to pass" Iruka finished picking up the papers in front of him and headed out the door as Misuki followed, soon Naruto left and went out side to see the happy faces of most of his class as they wore their new leaf headbands and their parents praising them on a job well done. Naruto then goes to the swing just out side the entrance. Not too long after that Misuki comes up to Naruto motioning him to come with him.

* A few hours later *

Naruto jumped down from a tree and landed with out a sound carrying a large scroll on his back, he then opens it up and looks inside, "_Kage Bushin no jutsu_ (_Shadow Clone Technique_)" Naruto read out loud "Well it looks like I can finally earn a clone technique." And immediately starts to practice. It's then some time later that Naruto sensed two presences coming towards him one in front and the other from behind. The one coming from right in front of him arrives first and he sees it's Iruka who looked _Pissed_.

"Found you Naruto." He said looking down at him, he then notices all the dirt marks on his clothes knowing that's a sign of training "What do you thing your doing?" he then asked

"Nothing much just caching a traitor." Said Naruto nonchalantly "You can come out now" he then said before a giant shuriken came flying out of the tree line from behind Naruto, who quickly side steps avoiding the object completely. Misuki then lands on one of the braches.

"Heh your smarter then you let on brat." He said with a palpable hatred in his voice.

"Misuki what are you doing?" Yelled Iruka stunted that a teacher would attack a student.

"I'm only doing my job, " he said to Iruka before turning to Naruto "Now why don't you give me the scroll before someone gets hurt."

"How about, " said Naruto trailing off before jumping with a fist cocked "no" he then punched Misuki sending him into another tree about fifteen meters back.

'What the hell' Misuki thought as he caught himself before touching the ground holing his ribs 'when was the brat this strong' before he could think of a plan Naruto came rushing at him putting him on the defensive. He started avoiding punches not wanting any of his bones to break like two of his ribs did from Naruto's punch earlier. Naruto then backed off five meters mid-punch.

"When I think where far enough away." Said Naruto getting an almost demonic look in his eyes.

"What are you talking about?" Asked Misuki in an almost frightened voice.

"Oh nothing really just this." Naruto said before his right arm started to pulsate as red and black tendrils came out of his shoulders and wrapped around his arm transforming it. The end result being where the elbow down, once was now is a now is a demonic looking blade. "_Uirusu:__Bureedo"_ (_Virus: Blade_). Naruto now stands over Misaki who fell to ground deathly terrified. Naruto raises his appendage and decapitates Misaki making a fountain of blood. The black tendrils then shot out of Naruto's other arm and Consume what's left. He then held his head as a memory rushes into it.

* Flashback *

"_Misaki I want you to infiltrate the Leaf village" said a very slimy voice_

"_And what else needs to be done my lord?" Misaki asked_

"_I need you get me the sacred scroll of sealing, as I did not have time to steal it when my foolish sensei found me."_

"_Yes, lord Orochimaru." Said Misaki leaving to prepare._

* End Flashback *

"So that who he's getting it for." Said Naruto to himself before returning to where the scroll was, to it and Iruka gone. Sighing he leave to give the Hokage his report.

* At the Hokage Tower *

Iruka is talking to the Hokage when Naruto walks in. he then bows and starts his report "Sir mission complete sir."

"Good now what happened?" he asked

"Yes sir," said Naruto "After leaving this office with the scroll I went to the area in the woods he had told me about, after about an hour of waiting Iruka shows up wondering why I took the scroll, not long after that Misaki showed you demanding the scroll." "I then went onto the attack leaving the scroll behind along with Iruka, then after getting far enough away I showed him my true power and killed him before consuming him, I then saw from his memory that he was working for Orochimaru who wanted the scroll for it's many forbidden jutsus." "I then went back to where I left the scroll, to find it gone along with Iruka, knowing he left to return the scroll." Finished Naruto.

"Good now you will be paid for a low B-ranked mission he said as he started to take out the money

"No need sir, I already enough payment, I learned the _Kage Bushin no Justu_." Said Naruto "Now if you will sir I need to get home for some sleep." He finished as he bowed and left.

"Now Iruka" said Sarutobi taking out his pipe "I do believe that Naruto has earned the right become a Genin of the village"

"Yes sir" said Iruka "I really was hoping that Naruto would pass as the number of students would not match the teams of students needed for every team this year."

"Good now I need you to deliver his headband to him" handing him a spare headband from his desk. Iruka takes it and leaves "Now lets see how you change this world, Naruto"

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Please review and read my other fics


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